Cobamp

Added
- Gene protein reaction rule evaluation module (cobamp.gpr.evaluators). Still a work in
progress but the aim is to eventually move all GPR code into this module
upon releasing a major revision
- New dependency (boolean.py)
Changed
- Fixed errors in the readthedocs quickstart example
- Corrected some assorted bugs on the ConstraintBasedModel and KShortest classes
Notice:
- This should be the last release without CI/CD

Changed
- Several bug fixes
- KShortest algorithm now adds constraints iteratively to avoid memory errors
- Several improvements to the ConstraintBasedModel class

Added
- Big-M indicators for solvers without a dedicated indicator constraint abstraction

Added
- SCIPY MAT format model reader
- Gene-protein-rule support with gene expression data integration functions
- Analysis functions (mainly frequency and graphs) with some plotting capability
- Transformer classes for algorithms that alter a metabolic network,
guaranteeing mapping between the reactions of both
- Higher-level classes (linear_systems module) for semi-efficient definition of LP problems based on Optlang
- Classes for evaluating and converting into postfix type arithmetic and boolean expressions

Changed
- Major code refactor. Module structure drastically changed and reorganized.
- Many bugfixes

Added
- Basic metabolic model classes for when an SBML file is not available or necessary
- Elementary flux pattern enumeration using the K-Shortest algorithm (as a wrapper)

Changed
- Entire package structure to accomodate other types of algorithms beyond the K-Shortest one

Removed
- Some modules that were too specific for the changes above

Added

- Base code for K-Shortest enumeration of EFMs and MCSs
- Core framework architecture (linear systems, algorithms and wrappers)
- COBRApy and framed model object readers